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PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm
Li, Xue-Qi1; Tan, Guang-Ming; Sun, Ning-Hui
2021
发表期刊JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
ISSN1000-9000
卷号36期号:1页码:56-70
摘要Genomic sequence alignment is the most critical and time-consuming step in genomic analysis. Alignment algorithms generally follow a seed-and-extend model. Acceleration of the extension phase for sequence alignment has been well explored in computing-centric architectures on field-programmable gate array (FPGA), application-specific integrated circuit (ASIC), and graphics processing unit (GPU) (e.g., the Smith-Waterman algorithm). Compared with the extension phase, the seeding phase is more critical and essential. However, the seeding phase is bounded by memory, i.e., fine-grained random memory access and limited parallelism on conventional system. In this paper, we argue that the processing-in-memory (PIM) concept could be a viable solution to address these problems. This paper describes "PIM-Align"-application-driven near-data processing architecture for sequence alignment. In order to achieve memory-capacity proportional performance by taking advantage of 3D-stacked dynamic random access memory (DRAM) technology, we propose a lightweight message mechanism between different memory partitions, and a specialized hardware prefetcher for memory access patterns of sequence alignment. Our evaluation shows that the proposed architecture can achieve 20x and 1 820x speedup when compared with the best available ASIC implementation and the software running on 32-thread CPU, respectively.
关键词accelerator design genomic sequence alignment near-memory computing
DOI10.1007/s11390-020-0825-3
收录类别SCI
语种英语
资助项目National Key Research and Development Program of China[2018YFB0204400] ; National Key Research and Development Program of China[2016YFB0201305] ; National Key Research and Development Program of China[2016YFB0200803] ; National Key Research and Development Program of China[2016YFB0200300] ; National Key Research and Development Program of China[XDC01030000] ; National Natural Science Foundation of China[6197237] ; National Natural Science Foundation of China[61702483] ; CAS[QYZDJ-SSW-JSC035]
WOS研究方向Computer Science
WOS类目Computer Science, Hardware & Architecture ; Computer Science, Software Engineering
WOS记录号WOS:000615566300005
出版者SCIENCE PRESS
引用统计
被引频次:13[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://119.78.100.204/handle/2XEOYT63/16163
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Li, Xue-Qi
作者单位1.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
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GB/T 7714
Li, Xue-Qi,Tan, Guang-Ming,Sun, Ning-Hui. PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm[J]. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,2021,36(1):56-70.
APA Li, Xue-Qi,Tan, Guang-Ming,&Sun, Ning-Hui.(2021).PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm.JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,36(1),56-70.
MLA Li, Xue-Qi,et al."PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm".JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY 36.1(2021):56-70.
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